In some cases, the main antagonist could be an old enemy of Naruto who has a personal vendetta. This enemy might have used his influence to get Naruto imprisoned and now that Naruto is free, they want to finish what they started. They would constantly try to undermine Naruto's attempts to regain his position and reputation in the village.
Perhaps the main antagonist is a corrupt official within the Hidden Leaf Village itself. This person was the one who arranged for Naruto's imprisonment in the first place and now that Naruto is out, they will do everything to stop him from uncovering their misdeeds. They might even team up with external enemies to achieve their goals.
It could be a corrupt ninja from another village who wants to get rid of Naruto as he sees him as a threat to his own plans. This ninja could have framed Naruto to send him to prison.
It could be a corrupt ninja from within the village who wants Naruto out of the way. Maybe someone jealous of Naruto's popularity and power, so they frame him and get him sent to prison. This antagonist would then try to keep Naruto in prison by any means necessary.
It could be the same people who framed Naruto and got him jailed in the first place. Maybe a group of rogue ninjas or corrupt village leaders who see Naruto as a threat to their power.
Perhaps Kaguya Otsutsuki is resurrected again, but this time with a stronger will and more dangerous plans. Since Naruto was the one who played a major role in defeating her before, she targets him first in this fanfiction.
It could be a powerful ninja from another village who saw Naruto as a threat even when he was in jail. This ninja might have been plotting to take over Konoha while Naruto was out of the picture. Now that Naruto is out and godlike, they see him as an even bigger obstacle to their plans.
It could be the warden of the Blood Prison. He might be a corrupt figure who is using the prison for his own gain. He sees Naruto as a threat to his operations and tries to keep him locked up at all costs.
It could be one of the powerful and corrupt prison guards. They might have their own hidden agendas and see Naruto as a threat to their power or secrets within the Blood Prison. So, they start a scheme to make it seem like Naruto has betrayed everyone.
The warden of the Blood Prison could be the main antagonist. He might be a power - hungry and corrupt individual who sees Naruto as a threat to his control over the prison. So, he devises plans to get rid of Naruto, which ultimately lead to Naruto's death.
Maybe a new, powerful and evil ninja from another land. This ninja could have come to the village and caused a lot of chaos, making Naruto believe that no one in his village was capable of protecting themselves or him. So he blames everyone for their weakness and starts to hate them all, with this new ninja being the root of the problem.
Another possibility is that there is no single main antagonist. It could be a combination of misunderstandings, village politics, and personal issues within Kurenai herself that lead to her betraying Naruto. For instance, the village elders might be pressuring Kurenai to keep Naruto in check, and at the same time, Kurenai has her own doubts about Naruto's power which could be misconstrued as a reason to betray him.